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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.29

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the CAPHEINE analysis pipeline.
        Report generated on 2025-08-05, 21:47 UTC based on data in: /home/hverdonk/work/d0/f047030769ca05e2ee144a56b1856f

        veg/CAPHEINE Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/veg/CAPHEINE

        Input/output options

        foreground_regexp
        cattle
        outdir
        CAPHEINE-H5N1
        reference_genes
        /home/hverdonk/GCF_000864105.1_noTerminalStopCodon.fasta
        unaligned_seqs
        /home/hverdonk/h5n1_outbreakSeqs.fasta

        Generic options

        trace_report_suffix
        2025-08-05_16-37-48

        Core Nextflow options

        configFiles
        /home/hverdonk/CAPHEINE/nextflow.config, /home/hverdonk/CAPHEINE/conf/silverback_arm.config
        container
        [MULTIQC:]
        launchDir
        /home/hverdonk
        profile
        standard
        projectDir
        /home/hverdonk/CAPHEINE
        runName
        big_edison
        userName
        hverdonk
        workDir
        /home/hverdonk/work

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        CAWLIGNcawlignnull
        DRHIPdrhip0.1.1
        HYPHY_BUSTEDhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_CLNhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_CONTRASTFELhyphyHYPHY 2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_FELhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_LABELTREE_REGEXPhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_MEMEhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_PRIMEhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        HYPHY_RELAXhyphy2.5.73(MP) for Linux on aarch64 ARM Neon SIMD zlib (v1.2.11)
        IQTREEiqtree2.4.0
        REMOVEAMBIGSEQSbiopython1.85
        python3.13.3
        SEQKIT_SPLITseqkit2.10.0
        WorkflowNextflow25.04.6
        veg/CAPHEINEv1.1

        CAPHEINE Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/veg/capheine

        Methods

        Data was processed using CAPHEINE v1.1 , which was written using the nf-core pipeline framework (Ewels et al., 2020). CAPHEINE utilises reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v25.04.6 (Di Tommaso et al., 2017) with the following command:

        nextflow run CAPHEINE -c CAPHEINE/conf/silverback_arm.config --reference_genes /home/hverdonk/GCF_000864105.1_noTerminalStopCodon.fasta --unaligned_seqs /home/hverdonk/h5n1_outbreakSeqs.fasta --foreground_regexp cattle --outdir CAPHEINE-H5N1

        Tools used in the workflow included: BioPython (Cock et al., 2009) BUSTED (Murrell et al., 2015) Cawlign Contrast-FEL (Kosakovsky Pond et al., 2020) DRHIP FEL (Kosakovsky Pond et al., 2005) HyPhy (Kosakovsky Pond et al., 2019) IQ-TREE (Minh et al., 2020) MEME (Murrell et al., 2012) MultiQC (Ewels et al., 2016) PRIME RELAX (Wertheim et al., 2014) SeqKit (Shen et al., 2024) .

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        • Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: Freely available python tools for Computational Molecular Biology and Bioinformatics. Bioinformatics. 2009 Mar 20;25(11):1422–3. doi:10.1093/bioinformatics/btp163
        • Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, et al. Gene-wide identification of episodic selection. Molecular Biology and Evolution. 2015 Feb 19;32(5):1365–71. doi:10.1093/molbev/msv035
        • Kosakovsky Pond SL, Wisotsky SR, Escalante A, Magalis BR, Weaver S. Contrast-FEL—a test for differences in selective pressures at individual sites among clades and sets of branches. Molecular Biology and Evolution. 2020 Oct 16;38(3):1184–98. doi:10.1093/molbev/msaa263
        • Kosakovsky Pond SL, Frost SD. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution. 2005 Feb 9;22(5):1208–22. doi:10.1093/molbev/msi105
        • Kosakovsky Pond SL, Poon AF, Velazquez R, Weaver S, Hepler NL, Murrell B, et al. Hyphy 2.5—a customizable platform for evolutionary hypothesis testing using phylogenies. Molecular Biology and Evolution. 2019 Aug 27;37(1):295–9. doi:10.1093/molbev/msz197
        • Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-tree 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution. 2020 Feb 3;37(5):1530–4. doi:10.1093/molbev/msaa015
        • Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Detecting individual sites subject to episodic diversifying selection. PLoS Genetics. 2012 Jul 12;8(7). doi:10.1371/journal.pgen.1002764
        • Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
        • Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. Relax: Detecting relaxed selection in a phylogenetic framework. Molecular Biology and Evolution. 2014 Dec 23;32(3):820–32. doi:10.1093/molbev/msu400
        • Shen W, Sipos B, Zhao L. Seqkit2: A Swiss Army knife for sequence and alignment processing. iMeta. 2024 Apr 5;3(3). doi:10.1002/imt2.191
        Notes:
        • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.